[Bio-software] Re: Consed: combine amplicons of same individual

Bastien Chevreux bach at chevreux.org
Fri Oct 6 16:50:46 EST 2006


Marian Thieme wrote:
> I have a question about the Alignment und Sequence editor Consed,
> because I want to evaluate and compare some sequence analysis tools to
> find out which one is best suited for a resequencing project: Is it
> possible to combine fragments/amplicons so that I get a contiguous
> sequence. I could imagine, that all fragments of a certain individual
> are placed in one line, so I can easly browse and edit the sequence for
> each individual. (Perhaps, overlapping fragments should be merged in
> some way). (At the moment I havent managed that, so all amplicons are
> treated seperatly.)

Hi Marian,

do you have sequences from one individual or from several? In the later
case, I am not sure whether there is a package that has exactly what you
want out of the box. In any way, consed (the editor) alone will probably
not help you as you would need an assembler (e.g. mira, phrap, cap3, etc.)
to go along with it.

Have you looked at the Staden package (http://staden.sourceforge.net/)? It's
*the* "swiss-army-knife" of assembly tools and is used for very small and
very large projects (millions of sequences). It has 
- a nice preprocessing package (pregap)
- a powerful editor (gap4 for contig editing, joining, splitting, annotation
  and much more) 
- and a number of very useful tools to complement certain needs (mutation
  detection etc.).
It also has some simple assemblers integrated, external assemblers can be
plugged into quite easily.

In your case, I could imagine that letting assemblers run on subsets of your
sequences (each one containing sequences from exactly one individual)
combine the results within gap4 might be what you need.

Regards,
  Bastien

-- 
        -- The universe has its own cure for stupidity. --
         -- Unfortunately, it doesn't always apply it. --



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